Newly Named Pew Scholar to Image Gut Bacteria with Sound Waves

Caltech's Mikhail Shapiro, assistant professor of chemical engineering, has been selected as a 2016 Pew scholar by the Pew Scholars Program in the Biomedical Sciences. As a Pew Scholar, Shapiro will receive $240,000 over the next four years in support of his research program to image the location and activities of microbes in the body using ultrasound.

Our guts, or intestines, are alive with colonies of bacteria. Some species are good for us but others are bad and can lead to medical conditions, such as food poisoning and irritable bowel disease. Observing these bacteria in action is difficult because they are hidden deep inside the body. Typically, researchers culture the microbes outside the body to learn more about them, but this does not reveal where the bacteria are in the gut, or how they interact.

Shapiro plans to solve this problem with bacteria genetically engineered to be visible to ultrasound. The same ultrasound imaging techniques used by doctors to take pictures of a developing baby could be used to visualize communities of bacteria in the gut.

"Imaging techniques that rely on photons, such as fluorescence or luminescence, don't penetrate very deeply into the body," says Shapiro. "We are developing proteins that cells can make that will allow them to interact with sound waves and magnetic fields, which can penetrate more deeply."

The key to the approach is a unique class of proteins normally employed by certain photosynthetic, single-celled organisms to control how much they float, a trait needed to regulate access to light and other nutrients. The proteins form gas-filled structures that, Shapiro's team discovered, can scatter sound waves in a manner that makes them detectable by ultrasound. The researchers plan to genetically engineer bacteria to produce the proteins, then image them in mice.

The technique could ultimately lead to better ways to diagnose conditions such as irritable bowel disease.

Shapiro came to Caltech from UC Berkeley in 2014. Before that, he was a postdoctoral fellow at the University of Chicago, and earned his PhD from the Massachusetts Institute of Technology.

The Pew Scholars Program in the Biomedical Sciences, according to their website, "provides funding to young investigators of outstanding promise in science relevant to the advancement of human health. The program makes grants to selected academic institutions to support the independent research of outstanding individuals who are in their first few years of their appointment at the assistant professor level."

In addition to engineering bacteria, Shapiro's lab works on other methods to image and control cells deep in our body—such as tumor cells, immune cells, and neurons—with ultrasound and magnetic resonance.